bwa mem -w option
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6.0 years ago
ibseq12 • 0

does anybody know what is the range of INT that can be used for the -w option of BWA Mem? (-w ) : INTBand width. Essentially, gaps longer than *INT will not be found. Note that the maximum gap length is also affected by the scoring matrix and the hit length, not solely determined by this option. [100]

thanks ib

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Just guessing, but isn't this the maximum gap length within a read to be reported in the same hit. Longer than this and the read alignment will be split and reported in a separate hit/line

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